Appendix J — Table Formatting – Data Skills for Reproducible Research

J.1 Data

First, let’s get some data. I’ve included a subset of data for the first nine pokemon from Dave Parr’s pokedex package. We have some character and numeric columns, plus some missing data (not all pokemon have a secondary type).

# devtools::install_github("DaveParr/pokedex")
# data from pokedex::pokemon

pokemon <- data.frame(
  id = 1:9, 
  name = c("Bulbasaur", "Ivysaur", "Venusaur",
           "Charmander", "Charmeleon", "Charizard",
           "Squirtle", "Wartortle", "Blastoise"),
  height = c(0.7, 1, 2, 0.6, 1.1, 1.7, 0.5, 1, 1.6),
  weight = c(6.9, 13, 100, 8.5, 19, 90.5, 9, 22.5, 85.5), 
  type_1 = c("grass", "grass", "grass", 
             "fire", "fire", "fire", 
             "water", "water", "water"), 
  type_2 = c("poison", "poison", "poison", 
             NA, NA, "flying", 
             NA, NA, NA)
)

J.2 Basic table

Look at how the table displays by default. This will display in one way in RStudio, but a different way when you render the document, so also render it and look at the HTML version.

pokemon

Table J.1: A default table display

id	name	height	weight	type_1	type_2
1	Bulbasaur	0.7	6.9	grass	poison
2	Ivysaur	1.0	13.0	grass	poison
3	Venusaur	2.0	100.0	grass	poison
4	Charmander	0.6	8.5	fire	NA
5	Charmeleon	1.1	19.0	fire	NA
6	Charizard	1.7	90.5	fire	flying
7	Squirtle	0.5	9.0	water	NA
8	Wartortle	1.0	22.5	water	NA
9	Blastoise	1.6	85.5	water	NA

Now see how it looks if you use flextable().

flextable(pokemon)

Table J.2: A basic flextable

id	name	height	weight	type_1	type_2
1	Bulbasaur	0.7	6.9	grass	poison
2	Ivysaur	1.0	13.0	grass	poison
3	Venusaur	2.0	100.0	grass	poison
4	Charmander	0.6	8.5	fire
5	Charmeleon	1.1	19.0	fire
6	Charizard	1.7	90.5	fire	flying
7	Squirtle	0.5	9.0	water
8	Wartortle	1.0	22.5	water
9	Blastoise	1.6	85.5	water

J.3 Cusomising tables

J.3.1 Subset/reorder columns

You can use the col_keys argument to select a subset of columns, or change their order. You can also do this with data wrangling before you send a data frame to flextable, but this can be easier in some instances.

flextable(pokemon, 
          col_keys = c("name", "weight", "height"))

Table J.3: Subsetting columns with col_keys

name	weight	height
Bulbasaur	6.9	0.7
Ivysaur	13.0	1.0
Venusaur	100.0	2.0
Charmander	8.5	0.6
Charmeleon	19.0	1.1
Charizard	90.5	1.7
Squirtle	9.0	0.5
Wartortle	22.5	1.0
Blastoise	85.5	1.6

J.3.2 Header

Use set_header_labels() to customise the header. You can change the name of one or more column.

flextable(pokemon) |>
  set_header_labels(id = "ID", 
                    name = "Name", 
                    height = "Height (m)", 
                    weight = "Weight (kg)",
                    type_1 = "Type 1", 
                    type_2 = "Type 2")

Table J.4: Customising the header with set_header_labels()

ID	Name	Height (m)	Weight (kg)	Type 1	Type 2
1	Bulbasaur	0.7	6.9	grass	poison
2	Ivysaur	1.0	13.0	grass	poison
3	Venusaur	2.0	100.0	grass	poison
4	Charmander	0.6	8.5	fire
5	Charmeleon	1.1	19.0	fire
6	Charizard	1.7	90.5	fire	flying
7	Squirtle	0.5	9.0	water
8	Wartortle	1.0	22.5	water
9	Blastoise	1.6	85.5	water

If you have headers that have a nested structure, and their names reflect this (like “category_instance1” and “category_instance2”), you can use separate_header() to separate them.

flextable(pokemon) |>
  separate_header() |>
  set_header_labels(type_1 = "primary", 
                    type_2 = "secondary")

Table J.5: Nesting the header with separate_header()

id	name	height	weight	type
id	name	height	weight	primary	secondary
1	Bulbasaur	0.7	6.9	grass	poison
2	Ivysaur	1.0	13.0	grass	poison
3	Venusaur	2.0	100.0	grass	poison
4	Charmander	0.6	8.5	fire
5	Charmeleon	1.1	19.0	fire
6	Charizard	1.7	90.5	fire	flying
7	Squirtle	0.5	9.0	water
8	Wartortle	1.0	22.5	water
9	Blastoise	1.6	85.5	water

Alternatively, you can manually add extra header rows.

flextable(pokemon) |>
  add_header_row(values = c("", "Measurements", "Types"),
                colwidths = c(2, 2, 2)) |>
  set_header_labels(type_1 = "primary", 
                    type_2 = "secondary")

Table J.6: Manually add a header row with add_header_row()

		Measurements		Types
id	name	height	weight	primary	secondary
1	Bulbasaur	0.7	6.9	grass	poison
2	Ivysaur	1.0	13.0	grass	poison
3	Venusaur	2.0	100.0	grass	poison
4	Charmander	0.6	8.5	fire
5	Charmeleon	1.1	19.0	fire
6	Charizard	1.7	90.5	fire	flying
7	Squirtle	0.5	9.0	water
8	Wartortle	1.0	22.5	water
9	Blastoise	1.6	85.5	water

J.3.3 Alignment

The defaults are usually correct, left-aligning text and right-aligning numbers, but you can also customise this using the align() function.

The code below centre aligns the first row of the header to “center”, and then right aligns the body cells in the “name” column.

flextable(pokemon) |>
  add_header_row(values = c("", "Measurements", "Types"),
                colwidths = c(2, 2, 2)) |>
  set_header_labels(type_1 = "primary", 
                    type_2 = "secondary") |>
  align(align = "center", i = 1, part = "header") |>
  align(align = "right", j = "name", part = "body")

		Measurements		Types
id	name	height	weight	primary	secondary
1	Bulbasaur	0.7	6.9	grass	poison
2	Ivysaur	1.0	13.0	grass	poison
3	Venusaur	2.0	100.0	grass	poison
4	Charmander	0.6	8.5	fire
5	Charmeleon	1.1	19.0	fire
6	Charizard	1.7	90.5	fire	flying
7	Squirtle	0.5	9.0	water
8	Wartortle	1.0	22.5	water
9	Blastoise	1.6	85.5	water

Note

See if you can figure out what i and j mean, using trial-and-error first, and the help function if you get stuck.

J.4 Themes

There are some built-in themes you can use.

J.4.1 Alafoli

flextable(pokemon) |> theme_alafoli()

Table J.7: The alafoli theme

id	name	height	weight	type_1	type_2
1	Bulbasaur	0.7	6.9	grass	poison
2	Ivysaur	1.0	13.0	grass	poison
3	Venusaur	2.0	100.0	grass	poison
4	Charmander	0.6	8.5	fire
5	Charmeleon	1.1	19.0	fire
6	Charizard	1.7	90.5	fire	flying
7	Squirtle	0.5	9.0	water
8	Wartortle	1.0	22.5	water
9	Blastoise	1.6	85.5	water

J.4.2 APA

flextable(pokemon) |> theme_apa()

Table J.8: The apa theme

id	name	height	weight	type_1	type_2
1	Bulbasaur	0.70	6.90	grass	poison
2	Ivysaur	1.00	13.00	grass	poison
3	Venusaur	2.00	100.00	grass	poison
4	Charmander	0.60	8.50	fire
5	Charmeleon	1.10	19.00	fire
6	Charizard	1.70	90.50	fire	flying
7	Squirtle	0.50	9.00	water
8	Wartortle	1.00	22.50	water
9	Blastoise	1.60	85.50	water

J.4.3 Booktabs

flextable(pokemon) |> theme_booktabs()

Table J.9: The booktabs theme

id	name	height	weight	type_1	type_2
1	Bulbasaur	0.7	6.9	grass	poison
2	Ivysaur	1.0	13.0	grass	poison
3	Venusaur	2.0	100.0	grass	poison
4	Charmander	0.6	8.5	fire
5	Charmeleon	1.1	19.0	fire
6	Charizard	1.7	90.5	fire	flying
7	Squirtle	0.5	9.0	water
8	Wartortle	1.0	22.5	water
9	Blastoise	1.6	85.5	water

J.4.4 Box

flextable(pokemon) |> theme_box()

Table J.10: The box theme

id	name	height	weight	type_1	type_2
1	Bulbasaur	0.7	6.9	grass	poison
2	Ivysaur	1.0	13.0	grass	poison
3	Venusaur	2.0	100.0	grass	poison
4	Charmander	0.6	8.5	fire
5	Charmeleon	1.1	19.0	fire
6	Charizard	1.7	90.5	fire	flying
7	Squirtle	0.5	9.0	water
8	Wartortle	1.0	22.5	water
9	Blastoise	1.6	85.5	water

J.4.5 Tron

flextable(pokemon) |> theme_tron()

Table J.11: The tron theme

id	name	height	weight	type_1	type_2
1	Bulbasaur	0.7	6.9	grass	poison
2	Ivysaur	1.0	13.0	grass	poison
3	Venusaur	2.0	100.0	grass	poison
4	Charmander	0.6	8.5	fire
5	Charmeleon	1.1	19.0	fire
6	Charizard	1.7	90.5	fire	flying
7	Squirtle	0.5	9.0	water
8	Wartortle	1.0	22.5	water
9	Blastoise	1.6	85.5	water

J.4.6 Tron Legacy

flextable(pokemon) |> theme_tron_legacy()

Table J.12: The tron_legacy theme

id	name	height	weight	type_1	type_2
1	Bulbasaur	0.7	6.9	grass	poison
2	Ivysaur	1.0	13.0	grass	poison
3	Venusaur	2.0	100.0	grass	poison
4	Charmander	0.6	8.5	fire
5	Charmeleon	1.1	19.0	fire
6	Charizard	1.7	90.5	fire	flying
7	Squirtle	0.5	9.0	water
8	Wartortle	1.0	22.5	water
9	Blastoise	1.6	85.5	water

J.4.7 Vader

flextable(pokemon) |> theme_vader()

Table J.13: The vader theme

id	name	height	weight	type_1	type_2
1	Bulbasaur	0.7	6.9	grass	poison
2	Ivysaur	1.0	13.0	grass	poison
3	Venusaur	2.0	100.0	grass	poison
4	Charmander	0.6	8.5	fire
5	Charmeleon	1.1	19.0	fire
6	Charizard	1.7	90.5	fire	flying
7	Squirtle	0.5	9.0	water
8	Wartortle	1.0	22.5	water
9	Blastoise	1.6	85.5	water

J.4.8 Vanilla

flextable(pokemon) |> theme_vanilla()

Table J.14: The vanilla theme

id	name	height	weight	type_1	type_2
1	Bulbasaur	0.7	6.9	grass	poison
2	Ivysaur	1.0	13.0	grass	poison
3	Venusaur	2.0	100.0	grass	poison
4	Charmander	0.6	8.5	fire
5	Charmeleon	1.1	19.0	fire
6	Charizard	1.7	90.5	fire	flying
7	Squirtle	0.5	9.0	water
8	Wartortle	1.0	22.5	water
9	Blastoise	1.6	85.5	water

J.5 Defaults

You can set a ton of defaults using set_flextable_defaults(). Do this at the top of your script and all of the tables in your document will have consistent styles.

set_flextable_defaults(digits = 2, 
                       font.size = 16, 
                       theme_fun = theme_apa,
                       na_str = "(none)")

flextable(pokemon)

id	name	height	weight	type_1	type_2
1	Bulbasaur	0.70	6.90	grass	poison
2	Ivysaur	1.00	13.00	grass	poison
3	Venusaur	2.00	100.00	grass	poison
4	Charmander	0.60	8.50	fire	(none)
5	Charmeleon	1.10	19.00	fire	(none)
6	Charizard	1.70	90.50	fire	flying
7	Squirtle	0.50	9.00	water	(none)
8	Wartortle	1.00	22.50	water	(none)
9	Blastoise	1.60	85.50	water	(none)

J.6 Next Steps

You can learn a lot more about how to customisie tables from the flextable book.

As a group, make a list of things you might want to do to tables, like highlight a row, add footnotes, include images, or set border styles.
Divide up the list and each create a short tutorial for how to accomplish the thing, using just the pokemon table.
Share your tutorial with the group!